Scan contig files against PubMLST typing schemes
☆282Mar 26, 2026Updated last month
Alternatives and similar repositories for mlst
Users that are interested in mlst are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Mass screening of contigs for antimicrobial and virulence genes☆493Apr 3, 2026Updated last month
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆261Dec 13, 2025Updated 5 months ago
- Rapid haploid variant calling and core genome alignment☆585Dec 12, 2025Updated 5 months ago
- BSR-Based Allele Calling Algorithm☆149May 15, 2026Updated last week
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆219Aug 27, 2025Updated 8 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Rapid prokaryotic genome annotation☆981Jan 6, 2026Updated 4 months ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 5 months ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆367May 10, 2026Updated last week
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆642May 15, 2026Updated last week
- Pairwise SNP distance matrix from a FASTA sequence alignment☆155Dec 31, 2025Updated 4 months ago
- Pan-genome wide association studies☆218May 29, 2024Updated last year
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆201May 5, 2026Updated 2 weeks ago
- Rapid large-scale prokaryote pan genome analysis☆379Nov 3, 2025Updated 6 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆95Mar 30, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A flexible pipeline for complete analysis of bacterial genomes☆512May 16, 2026Updated last week
- hybrid assembly pipeline for bacterial genomes☆641Jul 25, 2024Updated last year
- An updated pipeline for pangenome investigation☆358May 13, 2026Updated last week
- Assemble bacterial isolate genomes from Nanopore reads☆132Jan 22, 2025Updated last year
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆126Oct 30, 2023Updated 2 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆65Jun 5, 2025Updated 11 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆174Apr 16, 2025Updated last year
- SeqSero2☆40Oct 1, 2025Updated 7 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 14, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆27Aug 2, 2023Updated 2 years ago
- Short Read Sequence Typing for Bacterial Pathogens☆149Jun 20, 2021Updated 4 years ago
- whole genome MLST analysis☆53Mar 27, 2026Updated last month
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆87Dec 15, 2024Updated last year
- Antimicrobial Resistance Identification By Assembly☆187Oct 12, 2023Updated 2 years ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆156Oct 2, 2025Updated 7 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆179Apr 22, 2026Updated last month
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆416Updated this week
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆408Mar 2, 2026Updated 2 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆108Mar 2, 2026Updated 2 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆344Sep 11, 2025Updated 8 months ago
- a collection of scripts for organising bacterial genomes by species☆81Mar 18, 2022Updated 4 years ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆66May 5, 2023Updated 3 years ago
- Fast genome and metagenome distance estimation using MinHash☆443Sep 19, 2025Updated 8 months ago
- Making whole bacterial genome sequencing data analysis easy☆113Apr 22, 2025Updated last year
- ☆138May 11, 2026Updated last week